minimize water
  &cntrl
   imin=1,      ! flag to run minimization
   ntx=1,       ! default option to read coordinates but not velocities
   irest=0,     ! default option to not restart simulation instead run as new simulation
   maxcyc=10000,      ! maximum number of cycles of minimization
   ncyc=1000,     ! method of minimization switches from steepest descent to conjugate after ncyc cycles (default 10)
   ntpr=1000,   ! every ntpr steps, energy information gets printed to mdout & mdinfo files
   ntwr=1000,   ! every ntwr steps, the restrt file gets written
   cut=8.0,
   ntr=1,       ! flag for restraining specified atoms in Cartesian space; need to identify atoms with restraintmask
   restraintmask="!:WAT,NA,CL",  ! string specifying restrained atoms when ntr=1
   restraint_wt=50.0,  ! weight for positional restraints
   ntmin=1,     ! default for ncyc cycles, the steepest descent method is used and then conjugate gradient is switched on
/